VMD 1.9.2 Bugs, Limitations, and Workarounds

Alas, there are still bugs and inconsistancies in VMD. Following is
a list of known problems, limitations, and workarounds. For any issues
not specifically listed here, please be sure to check the
VMD release notes.

General

VMD will not draw ribbon or cartoon representations of cyclic proteins.
A test version of VMD is now available which
can correctly draw cyclic proteins. Until the new code is fully
tested it will remain an experimental feature, but we are happy to
provide it on request.

An incorrect PDB accession code or download failure causes a 0 atom
molecule to be loaded, though error messages are printed to indicate
the problem. Delete the extra molecule.

VMD contains a bug in the old "cartoon" representation, where
there are sometimes gaps between tubes and beta sheets.
Use the "NewCartoon" representation which doesn't have these problems.

Microsoft Windows Specific

Some combinations of video drivers and window operations can cause
VMD windows not to be redrawn properly when they are uncovered.
(believed to be an FLTK bug with expose events generated by the
Win32 text console window)
We believe this problem will be solved once and for all when we replace
the Win32 text console window with our own (based on TkCon, or FLTK).

The 'vmdmovie' plugin has problems compressing movies into
directories with names containing spaces, due to a bug with
the "VideoMach" program used to convert movies on Win32.

MacOS X Specific

Tk, and TkCon bugs:
Users running MacOS X on Intel based Macs have reported several bugs
that are attributed to the MacOS X version of Tk. The most serious of
these is a situation where TkCon becomes unresponsive and stops responding
to keystrokes. When this occurs, proper function can usually be
restored by selecting another application window (not VMD),
invoking the MacOS "expose" feature (press F9, or Fn-F9 on the keyboard),
and selecting the TkCon window again.
This will restore the keyboard focus to the TkCon window. Future versions
of VMD will use a newer Tcl/Tk version that we hope will fix this problem.

The Mac version of MSMS appears to misbehave when generating a surface
for some molecular structures. Specifically, loading the PDB '1hzx' does
not produce a surface on the Mac, though it works fine on other platforms.
Note: This is not a VMD bug, but is noted here for reference.

The MacOS X version of STRIDE fails to compute the secondary structure
for the system "1S5L" with the selection "protein".